[gmx-users] Invalid selection near '&' syntax error -- easy way to avoid?

Justin Lemkul jalemkul at vt.edu
Sat May 21 00:13:46 CEST 2016

On 5/20/16 5:54 PM, Christopher Neale wrote:
> Dear Users:
> I find that gmx make_ndx will create groups with names that have ampersands in them and that this complicates piping the group name back into an analysis tool. I have included an example below. There is an obvious solution with sed to rename the group in the .ndx file after creation (this is what I am doing now). However, I'm thinking about posting a redmine feature request since ideally I think the tool will not require an external step for name-based selection and I wanted to ask here first just in case I am missing something.

Groups can be renamed within make_ndx itself.  This does require you to know the 
group numbers ("name X mygroup", if you know X), but it's what I usually use 
since the number of default groups is predictable.


> ### commands
> {
>   echo "aC316 C216"
>   echo "aC316 C216 & r1-64"
>   echo "aC316 C216 & r65-128"
>   echo q
> } | gmx make_ndx -f start.gro -o rdf.ndx
> echo -e 'C316_C216_&_r_65-128\nC316_C216_&_r_65-128\n' | gmx rdf -f MD.xtc -n rdf.ndx -s MD.tpr
> ### output from gmx rdf:
>                     :-) GROMACS - gmx rdf, VERSION 5.1.2 (-:
>                             GROMACS is written by:
>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
>   Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen
>  Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner
>     Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
>    Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
>    Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers
>    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
>                            and the project leaders:
>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
> GROMACS:      gmx rdf, VERSION 5.1.2
> Executable:   /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
> Data prefix:  /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
> Command line:
>   gmx rdf -f MD.xtc -n rdf.ndx -s MD.tpr
> -------------------------------------------------------
> Program:     gmx rdf, VERSION 5.1.2
> Error in user input:
> Invalid selection 'C316_C216_&_r_65-128 '
>   Near '&'
>     syntax error
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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